State of the interactomes: an evaluation of molecular networks for generating biological insights.

Advancements in genomic and proteomic technologies have powered the creation of large gene and protein networks ("interactomes") for understanding biological systems. However, the proliferation of interactomes complicates the selection of networks for specific applications. Here, we present a comprehensive evaluation of 45 current human interactomes, encompassing protein-protein interactions as well as gene regulatory, signaling, colocalization, and genetic interaction networks.

Molecular detection of dengue virus from febrile patients in Ghana.

Background: Viral hemorrhagic fevers (VHFs) belong to a group of viral infectious diseases that interfere with the blood's clotting mechanism. VHF has a wide host range, including bats, rodents, or arthropods such as mosquitoes and ticks. Most VHFs emerge suddenly as outbreaks, making it difficult to predict occurrence.

Evaluation of large language models for discovery of gene set function.

Gene set enrichment is a mainstay of functional genomics, but it relies on gene function databases that are incomplete. Here we evaluate five large language models (LLMs) for their ability to discover the common functions represented by a gene set, supported by molecular rationale and a self-confidence assessment. For curated gene sets from Gene Ontology, GPT-4 suggests functions similar to the curated name in 73% of cases, with higher self-confidence predicting higher similarity.

Monitoring electrophilic intermediates in reactions of thiols in aqueous solution directly with F NMR.

Mechanistic studies of thiol reactivity can be challenging because electrophilic reaction intermediates, such as sulfenic acids (RSOH) and sulfenyl chlorides (RSCl), are generally too reactive to be observed directly. Herein we report the design and synthesis of a sterically-encumbered fluorinated triptycene thiol which enables direct observation of reaction intermediates in aqueous buffer by F NMR, as demonstrated in reactions with hydrogen peroxide and hypochlorous acid. Reactions with HO resulted in the formation of a persistent RSOH species, which was subsequently converted to a sulfinic acid (RSOH) and then a sulfonic acid (RSOH), while RSCl was found to be the intermediate in reactions with HOCl.